De novo mutations
Triodenovo was used to call de novo mutations:
- only SNP with GL/PL information was retained.
- only trios were used.
- filters: --minDP 7 --minDepth 10 and other default options
- Post filter:
- Basic filtering for SNVs. The following filter will retain sites of single nucleotides with only two alleles, QUAL>=30, and mutations in which parents are homozygous references and child is heterozygote with the heterozygote PL being zero, and the minimum PL of the other two genotypes in offering is 30 (i.e.ย the genotype likelihood, defined as P(R|G) in which R represents the aligned bases and G is the underlying genotype, of the called het mutation is >1000 than the genotype likelihood of the other two genotypes)
The scripts are stored in /30days/uqywan67/SSC/scripts/call_deno.R